GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dopDH in Shewanella amazonensis SB2B

Align Alpha-ketoglutaric semialdehyde dehydrogenase 1; alphaKGSA dehydrogenase 1; 2,5-dioxovalerate dehydrogenase 1; 2-oxoglutarate semialdehyde dehydrogenase 1; KGSADH-I; Succinate-semialdehyde dehydrogenase [NAD(+)]; SSDH; EC 1.2.1.26; EC 1.2.1.24 (characterized)
to candidate 6938534 Sama_2637 succinate-semialdehyde dehydrogenase (NAD(P)(+)) (RefSeq)

Query= SwissProt::Q1JUP4
         (481 letters)



>FitnessBrowser__SB2B:6938534
          Length = 480

 Score =  359 bits (921), Expect = e-103
 Identities = 191/468 (40%), Positives = 270/468 (57%), Gaps = 2/468 (0%)

Query: 9   TQLLIDGEWVDAASGKTIDVVNPATGKPIGRVAHAGIADLDRALAAAQSGFEAWRKVPAH 68
           T+  I+GEW DA SG+T+ + NPAT + I  V   G  +   A+AAA++   AWR + A 
Sbjct: 11  TKCYINGEWRDALSGETVTIANPATNEAIASVPVMGRDETREAIAAAEAALPAWRALTAK 70

Query: 69  ERAATMRKAAALVRERADAIAQLMTQEQGKPLTEARVEVLSAADIIEWFADEGRRVYGRI 128
           ER A +R+   L+ E AD +A +MT EQGKPL EA+ EV+ AA  IEWFA+E +R+YG  
Sbjct: 71  ERGAKLRRWYELMLENADDLALMMTTEQGKPLAEAKGEVVYAASFIEWFAEEAKRLYGDT 130

Query: 129 VPPRNLGAQQTVVKEPVGPVAAFTPWNFPVNQVVRKLSAALATGCSFLVKAPEETPASPA 188
           +P      +  V+K+ VG  AA TPWNFP   + RK   ALA GC+ +VK   +TP +  
Sbjct: 131 IPGHQGDKRIMVIKQGVGVTAAITPWNFPAAMITRKAGPALAAGCTMIVKPAPQTPFTAL 190

Query: 189 ALLRAFVDAGVPAGVIGLVYGDPAEISSYLIPHPVIRKVTFTGSTPVGKQLASLAGLHMK 248
           AL     +AG+P GV  +V GD   I + L  +PV+RK++FTGST VG +L       +K
Sbjct: 191 ALAELAAEAGIPPGVFSVVTGDAVAIGNELCENPVVRKLSFTGSTGVGIKLMQQCAPTLK 250

Query: 249 RATMELGGHAPVIVAEDADVALAVKAAGGAKFRNAGQVCISPTRFLVHNSIRDEFTRALV 308
           + ++ELGG+AP IV  DAD+  AV+ A  +K+RNAGQ C+   R  V + + D F + L 
Sbjct: 251 KVSLELGGNAPFIVFNDADLDAAVEGAMISKYRNAGQTCVCANRLYVQDGVYDAFAQKLA 310

Query: 309 KHAEGLKVGNGLEEGTTLGALANPRRLTAMASVIDNARKVGASIETGGERIGSEGNFFAP 368
                LKVGNG E G T G L N   L  + S + +A   GA++  GG+ +G  GNF  P
Sbjct: 311 AAVAKLKVGNGAEPGVTTGPLINAAALEKVQSHLQDALDKGATLVAGGKPLG--GNFMEP 368

Query: 369 TVIANVPLDADVFNNEPFGPVAAIRGFDKLEEAIAEANRLPFGLAGYAFTRSFANVHLLT 428
            ++ NV     V   E FGP+A +  F  +++ I +AN   FGLA Y + R  + +  + 
Sbjct: 369 AIVTNVDASMKVAREETFGPLAPLFRFSDVDDVIRQANDTEFGLAAYFYGRDISLIWKVA 428

Query: 429 QRLEVGMLWINQPATPWPEMPFGGVKDSGYGSEGGPEALEPYLVTKSV 476
           + LE GM+ +N         PFGG+K SG G EG    ++ Y+  K +
Sbjct: 429 EALEYGMVGVNTGLISTEVAPFGGMKSSGLGREGSKYGIDEYVEIKYI 476


Lambda     K      H
   0.318    0.134    0.393 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 594
Number of extensions: 18
Number of successful extensions: 2
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 481
Length of database: 480
Length adjustment: 34
Effective length of query: 447
Effective length of database: 446
Effective search space:   199362
Effective search space used:   199362
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 51 (24.3 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory